Manipulating the circadian clock to increase gene expression

ABSTRACT

A method of increasing gene expression by manipulating the circadian clock is described that includes transforming a photosynthetic organism to include an expression control sequence that modulates the expression of a clock gene to increase expression of a target gene. Photosynthetic organism having a modified circadian cycle reflecting this method are also described.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.14/933,622, filed Nov. 5, 2015, now U.S. Pat. No. 10,927,365, whichclaims priority to U.S. Provisional Patent Application Ser. No.62/076,040, filed Nov. 6, 2014, which is incorporated herein byreference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

The present invention was supported by grants from the NationalInstitute of General Medical Sciences (NIGMS RO1 GM067152 and RO1GM088595) and the U.S. Department of Energy (DE-FG36-05GO15027). TheGovernment has certain rights in this invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-Web and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Nov. 4, 2015, isnamed Circadian Regulation ST25 and is 30.2 kilobytes in size.

BACKGROUND

Circadian rhythms are circa-24 h oscillations in biological processesthat are controlled by an endogenous biochemical pacemaker to provide atemporal program that allows organisms to optimally adapt to the dailytransformation of environmental conditions. This “biological clock”rhythmically orchestrates intracellular activities that range from geneexpression, metabolism, cell division, to development and behavior. Ineukaryotes, approximately 10% of the genome is regulated by the dailyclock in any given tissue. In the photoautotrophic cyanobacteriumSynechococcus elongatus PCC 7942, virtually all gene expression iscontrolled at the level of promoter activity by the circadian clock (Liuet al., Genes Dev. 9, 1469-1478 (1995)), and 35-70% of steady-statetranscript abundances oscillate. Vijayan et al., Proc. Natl. Acad. Sci.USA 106, 22564-22568 (2009). The entire chromosome even undergoes dailycycles of topological change and compaction that are related to thisgenome-wide transcriptional control.

The KaiA, KaiB, and KaiC proteins form the central clockwork incyanobacteria, and the status of KaiC phosphorylation plays a key rolein the central clock mechanism as well as global regulation of outputgene expression. Gutu, A., and O'Shea, E. K., Mol. Cell 50, 288-294(2013). KaiC is both an autokinase and an autophosphatase, but KaiApromotes phosphorylation of KaiC (Iwasaki et al., Proc. Natl. Acad. Sci.USA 99, 15788-15793 (2002)) while KaiB combines with KaiA and KaiC toform a complex that promotes KaiC dephosphorylation. Qin et al., Proc.Natl. Acad. Sci. USA. 107, 14805-14810 (2010). There are multiplepathways that link the central KaiABC post-translational oscillator(PTO) to its transcriptional outputs that include the proteins SasA,CikA, LabA, RpaA, and RpaB. In particular, RpaA appears to be a majoroutput node that is regulated by KaiABC through independentSasA/CikA/LabA pathways. Taniguchi et al., Proc. Natl. Acad. Sci. USA107, 3263-3268 (2010). The global gene expression patterns in S.elongatus are primarily organized into two groups that are phased 180°apart. Liu et al., Genes Dev. 9, 1469-1478 (1995). The “Class I” or“subjective dusk” genes activate at dawn and rise throughout the day toa peak expression at dusk, while the “Class II” or “subjective dawn”genes turn on in the subjective night and peak at dawn. The Class I(subjective dusk) genes are the predominant group. It has been reportedthat overexpression of kaiC represses the rhythmic components of allgenes in the genome. Nakahira et al., Proc. Natl. Acad. Sci. USA 101,881-885 (2004). However, a more recent microarray analysis concludedthat kaiC overexpression represses the predominant Class I (dusk) genes,while up-regulating Class II (dawn) genes. Ito et al., Proc. Natl. Acad.Sci. USA 106, 14168-14173 (2009).

Insights into the regulation of gene expression in cyanobacteria areimportant for understanding the basic biology of circadian control, butalso have potential applications. Because they derive their energy fromthe sun and are genetically malleable, photoautotrophic cyanobacteriaare attractive bioreactors for synthesizing biofuels and otherbioproducts. Ducat et al., Trends in Biotech. 29, 95-103 (2011). Inparticular, S. elongatus has become one of the preferred platforms fordevelopment of this biotechnology. However, despite the appeal ofdirecting photosynthetic carbon fixation towards the production ofuseful molecules in cyanobacterial hosts, the efficiency of heterologousexpression achieved by cyanobacteria is currently too low for industrialapplication. Furthermore, few tools are available to reprogram metabolicflux in photosynthetic microbes along pathways towards the synthesis ofuseful bioproducts or their precursors. Wang et al., Front Microbiol. 3,344 (2012). Accordingly, there remains a need for methods and organismsin which the circadian clock is used to increase gene expression.

SUMMARY OF THE INVENTION

Due to the pervasive circadian control of promoter activities incyanobacteria, experimental modulation of clock genes could be exploitedto tune gene expression to operate maximally under constant-lightconditions or to resonate in harmony with periodic light-dark cycling.In this study, the inventors examined the phased expression patterns andfind that kaiA-vs. kaiC-overexpression (kaiA-OX vs. kaiC-OX) exhibitopposing actions over promoters such that the genome-wide patterns ofboth dusk (Class I) and dawn (Class II) genes can be explained. Theyrefer to the opposing actions of kaiA-OX vs. kaiC-OX as a “Yin-Yang”interdependency, based on the Taoist concept of balancing forces thatcomplementarily interact to promote harmony. This basic information wasused to reprogram circadian clock-controlled circuits to switch fromcycling to constitutive gene expression as well as manipulating theexpression of the kaiA gene to enhance expression of endogenous andforeign genes. As proof of principle, this strategy was applied towardsoptimizing the expression of endogenous and foreign [NiFe] hydrogenasesfor biohydrogen production and expression of foreign genes such asluciferase and human proinsulin, which serves as a test case forproduction of pharmaceuticals in cyanobacteria.

In one aspect, the invention provides a method of increasing geneexpression by manipulating the circadian clock, comprising transforminga photosynthetic organism to include an expression control sequence thatmodulates the expression of a clock gene to increase expression of atarget gene. In some embodiments, the photosynthetic organism is aplant, while in other embodiments the photosynthetic organism is aphotoautotrophic or photoheterotrophic bacteria, such as acyanobacteria.

Expression of the clock gene can be modulated in a variety of ways. Insome embodiments, the clock gene is selected from the group consistingof KaiA, KaiB, and KaiC. In another embodiment, the clock gene is KaiAor KaiC and the clock gene is overexpressed. In further embodiments, theexpression control sequence includes a promoter that is operably linkedto the clock gene. In some embodiments, the expression of the targetgene is operably linked to expression of the clock gene, while in otherembodiments modulating expression of a clock gene suppresses thecircadian rhythm of the photosynthetic organism. In a yet furtherembodiment, modulation of the clock gene is decreased expression of theclock gene, and the expression control sequence comprises a knockoutmutation.

The invention can be used to increase the expression of a variety ofdifferent target genes. In some embodiments, the target gene is abiofuel product or biofuel precursor expressing gene. In otherembodiments, the photosynthetic organism is a transgenic photosyntheticorganism, and the target gene is a heterologous gene. Examples ofheterologous genes include hydrogenase expressing genes and pro-insulinexpressing genes.

Another aspect of the invention provides a photosynthetic organismhaving a modified circadian cycle, comprising a photosynthetic organismthat has been transformed to include an expression control sequence thatmodulates the expression of a clock gene to increase expression of atarget gene. In some embodiments, the photosynthetic organism is aplant, while in other embodiments the photosynthetic organism is aphotoautotrophic or photoheterotrophic bacteria, such as acyanobacteria. The photosynethetic organisms can be modified to modulateclock gene expression using any of the methods described herein, toincrease the expression of any of the target genes described herein.

BRIEF DESCRIPTION OF THE FIGURES

The present invention may be more readily understood by reference to thefollowing drawings wherein:

FIGS. 1A-1D provide a construct and graphs showing the acute responsesof clock-controlled luminescence rhythm to kaiA-OX and its negligibleeffect on growth rate. (A) Constructs for luminescence reporting on theeffect of kaiA expression as used in panels B and C of this figure.Diagram shows the intact kaiABC locus, the psbAIp::luxAB reporterconstruct in NSI, and the IPTG-derepressible trcp::kaiA expressioncassette in NSII. (B) Rapid increase in luminescence expressionfollowing kaiA induction by IPTG at LL72 (=hour 72 in LL). (C) Doseresponse of kaiA-induced damping of the luminescence rhythms by varyingIPTG concentrations. IPTG was added at time 0 of LL. (D) kaiAoverexpression has no obvious effect on growth rate in various reporterstrains as indicated. In presence or absence of IPTG, the cells weregrown in LL at 30° C. with constant air bubbling and shaking. Celldensities were monitored by measuring OD₇₅₀ during growth. Data areaverages from two independent experiments for each strain.

FIGS. 2A-2E provide graphs and images showing the microarray profiles ofcycling genes in the kaiA-overexpressing (kaiA-OX) strain (A) Expressionprofiles of 800 cycling genes in the kaiA-OX strain in LL with orwithout 1 mM IPTG. These genes were sorted by peak time expressed bywild-type strains. The colors represent normalized data arranged indescending order, representing expression levels from high to low. Theaverage and S.D. over one cycle is 0.0 and 1.0, respectively. (B)Correlation of the level of induction for ˜800 circadian cycling genes.The expression level of each clock-controlled gene in Ptrc::kaiA cellsin the presence of IPTG at LL48 was compared with that in the absence ofIPTG at LL48. The abscissa indicates the fold induction by kaiAoverexpression at LL48. The ordinate indicates the fold induction bykaiC overexpression at LL33 for the same genes (regression line isR²=0.683). (C) Induction of KaiA up-regulates and down-regulatessubjective dusk and dawn genes, respectively. The expression level ofeach clock-controlled gene in trcp::kaiA cells in the presence of IPTGat LL48 was compared with that in the absence of IPTG at LL48. Theordinate shows the amount of induction of each gene by kaiA-OX, whilethe abscissa indicates the peak time of each of the 800 cycling genes inCircadian Time, (CTO/24=dawn, CT12=dusk). (D) and (E) Temporalexpression profiles of representative kaiA-enhanced subjective duskgenes (D) and kaiA-repressed subjective down genes (E) from microarrayanalysis. Expression profiles of genes in the kaiA-OX strain are shownwith or without 1 mM IPTG. The number in the ordinate indicates relativeexpression level.

FIGS. 3A-3C provides graphs showing the opposing responses of somerepresentative genes' expression to kaiA vs. kaiC overexpression andgenome-wide expression patterns regulated by kaiA-OX. (A & B) Microarraydata on mRNA abundances in response to kaiA vs. kaiC overexpression werecompared from continuous cultures of the kaiA-overexpressing strain(this work) and a previously reported kaiC-overexpressing strain (Xu etal., EMBO J. 19, 3349-3357 (2000)) in the presence or absence of IPTGapplied at LL24 (kaiA-OX strain) or LL25 (kaiC-OX strain). Five examplesof genes upregulated by kaiA overexpression but downregulated by kaiCoverexpression are shown in panel (A), and five examples of genesdown-regulated by kaiA overexpression but up-regulated by kaiCoverexpression in panel (B). The genes are identified on the right sideof each panel. (C) Spatial distribution of kaiA-OX-regulated geneexpression in the genome. Shown is the ratio of the expression level ofeach gene in trcp::kaiA cells in the presence of IPTG to that in theabsence of IPTG at hour 48 in LL. Each ratio was arranged in ascendingorder of Synpcc7942 gene number. Lower panel shows flanking regions toNeutral Site I (NS I) and their responses to kaiA-OX.

FIG. 4 provides a graph showing the spatial patterns of gene expressionalong the entire S. elongatus chromosome elicited by kaiA/kaiCoverexpression. The S. elongatus chromosome is circular, but it is hereshown in linear format with the expression levels of each gene inresponse to kaiA-OX or kaiC-OX. Changes of gene expression are shown asthe ratio of the transcript abundance in the presence of IPTG to that inthe absence of IPTG in LL. Each ratio was arranged in ascending order ofSynpcc7942 gene number (i.e., “1200” means gene “Synpcc7942_1200”). Thelower panel magnifies the region encompassing Synpcc7942_1565 toSynpcc7942_1583 where changes expression levels regulated by kaiA-OX andkaiC-OX are denoted. Increased gene expression in response to theindicated overexpression is classified as up-regulation (activation),whereas decreased transcript levels are considered down-regulation(repression).

FIGS. 5A and 5B provide graphs showing the expression of variouspromoter::luxAB reporter constructs in E. coli and S. elongatus. (A)Expression of luxAB luminescence reporters of various promoters in E.coli. Luminescence was measured from 0.5 ml of cells at a concentrationadjusted to OD=0.5 from E. coli cultures grown overnight. (B)Rhythmicity profiles of luxAB reporters driven by diverse promoters incyanobacteria. Following a 12 h dark treatment, luminescence rhythmswere monitored in LL in cultures of uniform cell density (30 μl atOD₇₅₀=0.3) placed on agar medium for the different promoter::reporterstrains. Corresponding promoters are as indicated. Note that the ordinalvalues are shown on a log₁₀ scale in arbitrary units of luminescence.“S.e. 7942” denotes S. elongatus PCC 7942.

FIGS. 6A-6G provide graphs showing that KaiA enhances expression of thecentral clock genes and E. coli promoters. (A) Constant kaiA-OXactivates expression of the central clock genes and attenuatesrhythmicity. Luminescence profiles were measured in a kaiA reporter(kaiAp::luxAB in NS I, i.e. kaiAp::lux) or kaiBC reporter (kaiBCp::luxABin NS I, i.e. kaiBCp::lux) co-expressing trcp::kaiA with or withoutIPTG. A final concentration of 1 mM IPTG was applied either at LL0 (hour0) or LL48 (hour 48) of constant light (LL) exposure. As a comparisonwith KaiC-induced repression, the kaiBC reporter strain (kaiBCp::luxAB,i.e. kaiBCp::lux) co-expressing trcp::kaiBC was performed in parallelfor IPTG application at LL48. (B) Northern blot assays for mRNAexpression of kaiA, kaiBC, and luxAB in the kaiA-overexpressing reporterstrain with or without IPTG in LL. (C) KaiA-OX enhances the abundance ofKaiB and KaiC proteins and hyper-phosphorylates KaiC. Cultures werecollected at Circadian Time 04 (CT04) in LL in presence of differentconcentrations of IPTG. Ratios of hyper-P KaiC to hypo-P KaiC are shownnumerically below the KaiC blots. The bottom row shows equivalentloading by Coomassie Brilliant Blue (CBB) staining. (D) kaiA-OX promotesconstant high expression of the luxAB luminescence driven by the E. coliconII promoter in the cyanobacterial reporter strain (conIIp::luxAB)co-expressing trcp::kaiA in the absence or presence of IPTG (i.e. H₂O[No IPTG] or 1 mM IPTG at LL0 or LL48). (E) Overall effect of kaiAoverexpression on conII promoter activity. Total luminescence units inLL for 7 days were collected from cultures of uniform cell density (30μl at OD₇₅₀=0.3) placed on agar medium from the conIIp::luxAB strainco-expressing trcp::kaiA in the absence (H₂O) or presence of 1 mMinducer (IPTG). (mean+/−S.D. for triplicates) (F) KaiA expressionpotentiates induction by the IPTG-derepressible heterologous trcpromoter. Luminescence expression profiles were compared between astrain harboring the trcp::luxAB reporter alone and a strainco-expressing both the trcp::luxAB reporter and trcp::kaiA in theabsence or presence of 1 mM IPTG added at LL48. (G) Co-induction of thereporter activities by the IPTG and KaiA in the trcp::luxAB reporterstrain co-expressing trcp::kaiA in the absence (No IPTG) or in thepresence of 1 mM IPTG started at LL0 or LL48. Note the log₁₀ scale forthe ordinate.

FIGS. 7A-7F provides graphs showing that overexpression of kaiA enhancesexpression of the central kai clock genes. (A & B) Comparison ofluminescence expression profiles between reporter strains for twodifferent kai promoters (kaiBCp::luxAB or kaiAp::luxAB) alone andstrains with the same reporters co-expressing trcp::kaiA in the absenceor presence of 1 mM IPTG in LL applied at day 0 or day 2. (A)kaiBCp::luxAB reporter alone vs. kaiBCp::luxAB strain co-expressingtrcp::kaiA. (B) kaiAp::luxAB reporter alone vs. kaiAp::luxAB strainco-expressing trcp::kaiA. (C) Densitometry of the Northern blotting datashown in FIG. 6B. Results from two separate experiments are shown (oneof which is depicted in FIG. 6B) and the lines connect the averages ofthese replicates. (D) qRT-PCR analysis of kaiBC mRNA activation by kaiAoverexpression. Cells from wild-type (WT) or kaiA-overexpressing(kaiA-OX) strains were released to LL after 2 two cycles of 12 h LD. AtLL24, 1 mM IPTG was added and cells were collected at LL34 for qRT-PCRassays for kaiBC mRNA. (E) Hyper-induction of {ATG}KaiA protein by IPTGand its enhancement of KaiB and KaiC protein abundances. The culturesfrom {ATG}kaiA-OX strain or wild-type strain (WT) were collected at CT12in LL in presence of different concentrations of IPTG. Equal loadingswere confirmed by the non-specific bands (NB) to KaiB. At CT12, KaiC isalready mostly hyper-phosphorylated, and induction of {ATG}kaiAincreases KaiC abundance while maintaining its hyperphosphorylationstatus. Note that the {ATG}kaiA overexpression construct with an ATGstart codon is slightly “leaky,” and even at 0 μM IPTG, there is someextra expression of KaiA that increases KaiB and hyper-P KaiC levelsabove the WT control. (F) Densitometry of the immunoblot data shown inpanel E.

FIGS. 8A-8C provide graphs showing that KaiA promotes expression andactivity of endogenous Hox hydrogenase (H₂ase). (A) kaiA-enhanced mRNAmicroarray profiles of all H₂ase subunits and H₂ase maturation genes (asdenoted) in the kaiA-overexpressing strain with or without IPTG. (B)Hydrogenase activity increases in the {ATG}kaiA-OX strain relative tothe wild-type (WT) strain in the absence or presence of IPTG induction.Data are represented as mean+/−SD from three independent experiments andanalyzed with t-test. Note that the {ATG}kaiA overexpression constructis slightly “leaky”, and even at 0 μM IPTG, there is some extraexpression of KaiA above that in WT. (C) KaiA causes constantly highlevels of hydrogenase activities under continuous light conditions.Following a 12 h of dark pulse, the endogenous hydrogenase activitieswere measured from samples of the WT and {ATG}kaiA-OX strains at theindicated times in LL.

FIGS. 9A and 9B provide a diagram and graphs showing the additionalenhancement of the IPTG-inducible trc promoter by kaiA overexpression.(A) Diagram of the trc/kaiA strain coexpressing trcp::kaiA in NS II witha kanamycin resistance marker and trcp::luxAB reporter in NS I with aspectinomycin resistance marker. (B) Luminescence expression profileswere compared between strain harboring the trcp::luxAB reporter andstrain co-expressing both the trcp::luxAB reporter and trcp::kaiA in theabsence (No IPTG) or presence of 1 mM IPTG added at LL0.

FIGS. 10A-10I provide graphs and images showing that KaiA enhancesexpression and accumulation of foreign genes and proteins. (A)Accumulation of Vibrio harveyi luciferase (Lux) was enhanced byinduction of kaiA with or without IPTG (0, 15, 500 μM IPTG) in thestrain co-expressing psbAIp::luxAB and trcp::{ATG}kaiA. A constitutivenonspecific band is marked “nb.” (B) Densitometry of the V. harveyi Luxabundance from the immunoblot in panel A, which was calculated from theratio of Lux:nb abundance (1=Lux:nb at 0 μM IPTG). (C) KaiA enhancesexpression of heterologous hydrogenases. Immunoblot assays forexpression of HynL, KaiA, and KaiC in strains of the wild type, RC41,and RC41 co-expressing trcp::{ATG}kaiA (i.e RC41/kaiA-OX) with (20 μM)or without IPTG (0 μM) for 24 hours. The top row shows bothKaiA-enhanced and IPTG-induced expression of the large subunit (HynL,˜69 kDa) of the A. macleodii hydrogenase. “nb” denotes a nonspecificband recognized by the antisera raised against Thiocapsa roseopersicinaHynL, which was used as an internal control for quantitative analyses ofHynL expression levels. The 2^(nd) and 3^(rd) rows confirm the KaiAoverexpression and its enhancement of the hyperphosphorylated KaiCexpression in the RC41/kaiA-OX strain. The bottom row shows equivalentloading by CBB staining. Note that the kaiA overexpression constructwith an ATG start codon is slightly “leaky” with a higher expressionlevel as compared with WT even without IPTG induction. (D) Densitometryof expression levels of the A. macleodii hydrogenase subunit HynL fromthe top panel of (C). Ratios of the HynL/nb signals are averages withstandard deviations from three experiments. ** p<0.001 in a pairedt-test. (E) Activity of the foreign A. macleodii hydrogenase in S.elongatus. After 24 h induction by 20 μM IPTG in light, the hydrogenaseactivities were determined. Data are the averages with S.D. from fourindependent experiments, and the hydrogenase activities in the RC41 andRC41/kaiA-OX strains were shown as ratios of the values as compared withwild type. (F) KaiA enhances accumulation of human proinsulin protein(GST::HPI fusion protein) in LD and LL (time 0=beginning of light; LD=12h light/12 h dark cycle). Cells expressing conIIp::GST-HPI (GST-HPI/WT)or co-expressing conIIp::GST-HPI and trcp::{ATG}KaiA (GST-HPI/KaiA) weregrown in the presence of 1 mM IPTG and collected at indicated LD and LLtime points. The immunoblot assay for the fusion protein GST::HPI wasperformed using a monoclonal antibody against GST. “nb” denotes anonspecific band recognized by the GST antibody. (G) Densitometry of theGST-HPI expression levels from the data of panel (F). Abscissa: blackbar indicates the dark portion of a light/dark (LD) cycle, and the whitebar indicates illumination in LD or LL. (H) Constant enhancement of theGST::HPI production by kaiA overexpression in DD. The LL-grown cellsfrom the strains GST-HPI/WT or GST-HPI/KaiA were given a 12 h darktreatment, then 1 mM IPTG was applied at lights-on. After an additional12 h growth in light, the cultures were transferred to constant darknessin a shaking water bath with bubbling and cells were collected every 6h. “nb” denotes a nonspecific band recognized by the GST antibody. (I)Densitometry of the GST-HPI expression levels from two experiments inDD.

FIGS. 11A-11F provide graphs and images showing the application of kaiAmanipulation to foreign gene expression. (A) Diagram of the trcp-drivenexpression cluster coding for the A. macleodii Deep Ecotype [NiFe]hydrogenase HynSL and 11 surrounding accessory proteins cloned into theNS I site of the endogenous hoxYH-knockout mutant (i.e. the RC41strain). (B) Neither deletion of endogenous hoxYH genes noroverexpression of foreign Alteromonas macleodii hydrogenase clustergenes has a considerable effect on circadian luminescence rhythms.Luminescence rhythms in WT, ΔHOX, and RC41 strains in LL with or withoutIPTG application. Following a 12 h dark exposure to synchronize clocksamong the cells in the population, luminescence rhythms were monitoredin different strains with a psbAIp::luxAB reporter in NS II in LL.WT=wild type strain of the S. elongatus PCC 7942. ΔHOX=knock-out ofendogenous hoxYH genes. RC41=S. elongatus ΔHOX mutant co-expressing A.macleodii hydrogenase cluster genes in NS I. (C) KaiA overexpression andits enhancement of KaiC expression in the hoxYH-null mutant strainco-expressing A. macleodii hydrogenase cluster genes and the kaiA-OXconstruct. WT (S.e. 7942)=wild type strain of the S. elongatus PCC 7942.RC41=HoxYH-knockout mutant co-expressing A. macleodii hydrogenasecluster genes. RC41+kaiA-OX=RC41 strain co-expressing trcp::{ATG}kaiA.KaiA and KaiC protein abundance levels in different strains with (20 μM)or without IPTG (0 μM) are shown in the upper and lower panels,respectively. (D-F) KaiA enhances expression of the GST-HPI fusionprotein in constant light. (D) Diagram of the trcp-driven expression ofthe foreign coding fusion for the GST tag and human proinsulin. Thelinker sequence between GST and HPI is shown. (E) Immunoblot assay forthe GST-HPI fusion protein was performed using a monoclonal antibodyagainst GST. Cells expressing conIIp::GST-HPI (GST-HPI/WT) orco-expressing conIIp::GST-HPI & trcp::{ATG}kaiA (GST-HPI/KaiA) weregrown in the presence of 1 mM IPTG and collected at the indicated timepoints in LL. The wild-type strain (WT) and transgenic strain expressingGST alone (GST/WT), grown in LL, were used as controls. “nb” denotes anonspecific band in the same blot recognized by the GST antibody. (F)Densitometry of the GST-HPI expression levels from the panel of (E).

FIGS. 12A-12C provide graphs and a scheme showing complementaryregulation by KaiA and KaiC and its manipulation to globally reprogramgene expression. (A) By constantly overexpressing kaiA (kaiA-OX),subjective dusk (Class I) genes are up-regulated (Class II subjectivedawn genes are down-regulated) and rhythmicity of gene expression islost. This gene expression pattern (curve) mimics that of subjectivedusk genes (peak expression of the kaiBC gene) during the normal rhythm.Constant overexpression of kaiC (kaiC-OX) has the opposite effects onClass I vs. II gene expression and represses activity of subjective duskgenes. (B) These complementary gene expression patterns are mediated bythe central circadian clock that is composed of a post-translationaloscillator (PTO) that regulates the oscillation of KaiC phosphorylationstatus, leading to a Yin-Yang output of global gene expression(including kaiABC expression) where hyperphosphorylated KaiCup-regulates dusk (Class I) genes and hypophosphorylated KaiCup-regulates dawn (Class II) genes. Overexpression of kaiA vs. kaiC canlock the Yin-Yang patterns into either dusk phase (kaiA-OX) or dawnphase (kaiC-OX). The KaiABC PTO cycles the phosphorylation status ofKaiC (hexamers) as regulated by interactions with KaiA (dimers) and KaiB(monomers). (C) Latching the Yin-Yang pattern into dusk phase by kaiA-OXenhances the expression of dusk genes—including heterologous genesinserted into NSI or NSII—and leads to a greater accumulation of geneproducts in constant light (LL) as shown by the cross-hatched area thanwould be possible if the same gene were expressed under control of thenative rhythmic system.

FIGS. 13A-13C provide graphs showing that manipulation of mutantvariants of the negative component KaiC also constantly enhances geneexpression. A. Comparison of psbAIp::luxAB rhythmicity and expressionlevels between wild-type KaiC strain (KaiC/WT) and double mutant KaiCstrain (KaiC/A422V/H423N) in constant light without any specialtreatment (such as an inducer like IPTG). Two replicate examples areshown for each strain. B. The expression patterns of the psbAIp::luxABreporter in the wild-type strain (WT) alone and in overexpressingstrains with different versions of KaiC under the control of theIPTG-inducible trc promoter (KaiC/WT-OX=trcp::wild-type kaiC;KaiBC/WT-OX=trcp::wild-type kaiB & kaiC; KaiC/EE-OX=trcp::double mutantkaiC/S431E-T432E. In constant light (LL), when IPTG was applied at hourLL24, overexpression of either wild-type KaiC or KaiB & KaiC constantlyrepresses the reporter expression, whereas overexpression of the doublemutant KaiC/EE continuously boosts the luminescence expression. C.Overexpression of the double mutant KaiC/EE constantly enhancesabundance of the foreign luciferase protein. Top panel shows immunoblotsof Vibrio harveyi luciferase protein (LuxA) in thepsbAIp::luxAB-expressing wild-type strain (WT) and a KaiC-manipulatedstrain with trcp::KaiC/EE (WT/KaiC-EE/OX) in constant light with orwithout 0.1 mM IPTG. The luciferase protein signal is indicated by“LuxA,” and a constitutive nonspecific band is marked “nb.” Bottom panelis the densitometry of the V. harveyi LuxA abundance from theimmunoblots above, which was calculated from the ratio of LuxA:nbabundance.

FIGS. 14A and 14B provides graphs showing that constant high expressionof the reporter gene in a strain in which an input pathway component ofthe circadian system (cikA) has been genetically knocked out (A or nullstrain). In this case, no treatment with an inducer (such as IPTG) isnecessary to achieve high output gene expression. A. Luminescenceexpression profiles of the wild-type strain (WT) and cikA-null strain(CikA null) in constant conditions. B. Total expression levels inconstant light for 7 days were calculated as luminescence units perminute in wild-type strain (WT) and cikA-knockout strain (ΔCikA). **p<0.001.

To illustrate the invention, several embodiments of the invention willnow be described in more detail. Skilled artisans will recognize theembodiments provided herein have many useful alternatives that fallwithin the scope of the invention.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a method of increasing gene expression bymanipulating the circadian clock is that includes transforming aphotosynthetic organism to include an expression control sequence thatmodulates the expression of a clock gene to increase expression of atarget gene. Photosynthetic organisms having a modified circadian cyclereflecting this method are also described.

Definitions

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. In case of conflict, thepresent specification will control.

The terminology as set forth herein is for description of theembodiments only and should not be construed as limiting of theinvention as a whole. Unless otherwise specified, “a,” “an,” “the,” and“at least one” are used interchangeably. Furthermore, as used in thedescription of the invention and the appended claims, the singular forms“a,” “an,” and “the” are inclusive of their plural forms, unlesscontraindicated by the context surrounding such. The singular “plant” islikewise intended to be inclusive of the plural “plants.”

The terms “comprising” and variations thereof do not have a limitingmeaning where these terms appear in the description and claims.

The term “polynucleotide” or “nucleic acid molecule” refers to apolymeric form of nucleotides of at least 10 bases in length. The termincludes DNA molecules (e.g., cDNA or genomic or synthetic DNA) and RNAmolecules (e.g., mRNA or synthetic RNA), as well as analogs of DNA orRNA containing non-natural nucleotide analogs, non-nativeinter-nucleoside bonds, or both. The nucleic acid can be in anytopological conformation. For instance, the nucleic acid can besingle-stranded, double-stranded, triple-stranded, quadruplexed,partially double-stranded, branched, hair-pinned, circular, or in apadlocked conformation.

The term “gene” as used herein refers to a nucleotide sequence that candirect synthesis of an enzyme or other polypeptide molecule (e.g., cancomprise coding sequences, for example, a contiguous open reading frame(ORF) which encodes a polypeptide) or can itself be functional in theorganism. A gene in an organism can be clustered within an operon, asdefined herein, wherein the operon is separated from other genes and/oroperons by intergenic DNA. Individual genes contained within an operoncan overlap without intergenic DNA between the individual genes.

The term “polypeptide” encompasses both naturally-occurring andnon-naturally-occurring proteins, and fragments, mutants, derivativesand analogs thereof. A polypeptide may be monomeric or polymeric.Further, a polypeptide may comprise a number of different domains eachof which has one or more distinct activities.

The term “expression” when used in relation to the transcription and/ortranslation of a nucleotide sequence as used herein generally includesexpression levels of the nucleotide sequence being enhanced, increased,resulting in basal or housekeeping levels in the host cell,constitutive, attenuated, decreased or repressed.

The term “vector” or “expression vector” refers to any type of geneticconstruct comprising a nucleic acid coding for a RNA capable of beingtranscribed. Expression vectors can contain a variety of controlsequences, structural genes (e.g., genes of interest), and nucleic acidsequences that serve other functions as well.

The term “expression control sequence” as used herein refers topolynucleotide sequences which are necessary to affect the expression ofcoding sequences to which they are operatively linked. Expressioncontrol sequences are sequences which control the transcription,post-transcriptional events and translation of nucleic acid sequences.Expression control sequences include appropriate transcriptioninitiation, termination, promoter and enhancer sequences; efficient RNAprocessing signals such as splicing and polyadenylation signals;sequences that stabilize cytoplasmic mRNA; sequences that enhancetranslation efficiency (e.g., ribosome binding sites); sequences thatenhance protein stability; and when desired, sequences that enhanceprotein secretion. The nature of such control sequences differsdepending upon the host organism; in prokaryotes, such control sequencesgenerally include promoter, ribosomal binding site, and transcriptiontermination sequence. The term “control sequences” is intended toinclude, at a minimum, all components whose presence is essential forexpression, and can also include additional components whose presence isadvantageous, for example, leader sequences and fusion partnersequences.

The term “transformed,” as used herein, refers to a cell into which hasbeen introduced a nucleic acid molecule by molecular biology techniques.As used herein, the term transformation encompasses all techniques bywhich a nucleic acid molecule might be introduced into such a cell,including transfection with viral vectors, transformation with plasmidvectors, and introduction of naked DNA by electroporation, lipofection,and particle gun acceleration.

The term “recombinant,” as used herein, refers to a nucleic acid is onethat has a sequence that is not naturally occurring or has a sequencethat is made by an artificial combination of two otherwise separatedsegments of sequence. This artificial combination can be accomplished bychemical synthesis or, more commonly, by the artificial manipulation ofisolated segments of nucleic acids, e.g., by genetic engineeringtechniques.

The term “recombinant host cell” (or simply “host cell”), as usedherein, is intended to refer to a cell into which a recombinant vectorhas been introduced. It should be understood that such terms areintended to refer not only to the particular subject cell but to theprogeny of such a cell. Because certain modifications may occur insucceeding generations due to either mutation or environmentalinfluences, such progeny may not, in fact, be identical to the parentcell, but are still included within the scope of the term “host cell” asused herein. A recombinant host cell may be an isolated cell or cellline grown in culture or may be a cell which resides in a living tissueor organism.

A “transgenic photosynthetic organism,” as used herein, refers to aphotosynthetic organism (e.g., photosynthetic plant or bacteria) thatcontains recombinant genetic material not normally found in organisms ofthis type and which has been introduced into the organism in question(or into progenitors of the plant) by human manipulation. Thus, forexample, a plant that is grown from a plant cell into which recombinantDNA is introduced by transformation is a transgenic plant, as are alloffspring of that plant that contain the introduced transgene (whetherproduced sexually or asexually).

The term “operably linked” refers to the arrangement of variouspolynucleotide elements relative to each other such that the elementsare functionally connected and are able to interact with each other.Such elements may include, without limitation, a promoter, an enhancer,a polyadenylation sequence, one or more introns and/or exons, and acoding sequence of a gene of interest to be expressed. “Operably linked”expression control sequences refers to a linkage in which the expressioncontrol sequence is contiguous with the gene of interest to control thegene of interest, as well as expression control sequences that act intrans or at a distance to control the gene of interest.

The term “modulation” means in relation to expression or geneexpression, a process in which the expression level is changed by saidgene expression in comparison to the control organism, the expressionlevel may be increased or decreased. The original, unmodulatedexpression may be of any kind of expression of a structural RNA (rRNA,tRNA) or mRNA with subsequent translation. The term “modulating theactivity” shall mean any change of the expression of the inventivenucleic acid sequences or encoded proteins, which leads to increasedexpression of a target gene.

Methods of Increasing Gene Expression by Manipulating the CircadianClock

In one aspect, the invention provides a method of increasing geneexpression by manipulating the circadian clock. The method includestransforming a photosynthetic organism to include an expression controlsequence that modulates the expression of a clock gene to increaseexpression of a target gene.

Expression of the target gene can be increased in two different ways. Insome embodiments, the expression of the target gene is operably linkedto expression of the clock gene. For example, expression of the clockgene can increase the activity of a promoter associated a target gene.In any case, in these embodiments, increased or decreased expression ofthe clock gene has a relatively direct effect on increasing expressionof the target gene.

In another embodiment, modulating expression of a clock gene suppressesthe circadian rhythm of the photosynthetic organism. The circadianrhythm is a cyclic pattern of activity for the photosynthetic organism,which reflects the modulation of gene expression occurring in responseto operation of the circadian clock. By suppressing the circadianrhythm, the photosynthetic organism can be “locked” into a single state,in which expression of the target gene is occurring at a high state. Inthis embodiment, expression of the target gene is not necessarilyoperably linked to expression of the clock gene, but rather is effectedby the overall state of the cell, with regard to its position in thecircadian cycle.

The expression control sequence is a polynucleotide sequence thatmodulates the expression of a clock gene. An example of an expressionvector including an expression control sequence is shown in FIG. 1A.Preferably, the expression vector or vectors include an expressioncontrol sequence to increase expression of a clock gene, the clock genewhose expression is being increased, and other sequences known to thoseskilled in the art for use in expression vectors, such as selectionmarkers. The expression vectors shown in FIG. 1A are flanked withneutral site (NS I and NS II) sequences to allow for homologousrecombination into neutral site I (GenBank accession number U30252) orneutral site II (GenBank accession number U44761), which are sites wherethe S. elongates chromosome can be disrupted without any discernibleeffect on the phenotype. Vectors used for these neutral sites includethe NS1 vector pAM1303 (SEQ ID NO: 1) and the NS 2 vector pAM1579 (SEQID NO: 2), shown in FIG. 1.

A clock gene is a gene in an organism such as a photosynthetic organismthat is involved in regulation of the circadian rhythm. Becausephotosynthetic organisms in particular thrive when they optimize themetabolism to the ups and downs of the daily cycle set by the sun, clockgenes play an important role in photosynthetic organisms. See Johnson C.H., Annu Rev Physiol. 63:695-728 (2001). For a review of bacterialcircadian programs, see Johnson C. H., Cold Spring Harb Symp Quant Biol.72:395-404 (2007).

The specific clock genes involved in regulating the circadian rhythm candiffer in different types of photosynthetic organisms. Accordingly, insome embodiments, the clock genes are plant clock genes. In furtherembodiments, the plant clock genes are algal clock genes. In otherembodiments, the clock genes are photosynthetic bacteria clock genes. Ina yet further embodiment, the clock genes are cyanobacterial clockgenes. The specific clock genes for particular organisms are known tothose skilled in the art.

In some embodiments, the clock gene is selected from the groupconsisting of KaiA (SEQ ID NO: 3), KaiB (SEQ ID NO: 4), and KaiC (SEQ IDNO: 5), and homologs thereof. These genes are part of the gene clusterkaiABC that control the circadian rhythm in cyanobacteria. See GenBanknumber AB010691, and Ishiura et al., Science 281, 1519-1523 (1998). Forexample, in some embodiments, the clock gene is KaiA or KaiC and theclock gene is overexpressed.

Other plant clock genes are known to those skilled in the art. TOC1 is aclock gene identified in Arabidopsis. Transient induction of TOC1expression with ethanol using an ALC::TOC1 line caused upregulation of1254 output genes. Gendron et al., PNAS, 109(8):3167-72 (2012). AnotherArabidopsis clock gene is CCA1. Nagel et al. overexpressed CCA andanalyzed RVE1 and HEMA1 expression. RVE1 has an increase in expressionat some specific phases under LD conditions. Nagel et al., PNAS,112(34):E4802-10 (2015). Another Arabidopsis clock gene is PRR7. Liu etal., 2013, shows that the triple mutant prr5 prr7 prr9 constitutivelyupregulate cold-stress inducible genes such as CBF2 and CBF3. Liu etal., Plant J. 76(1):101-14 (2013). The prr5/prr7/prr9 mutant also showsupregulation of day genes and dowregulation of night genes. Nakamichi etal., Plant Cell Physiol., Plant Cell Physiol. 50(3):447-62 (2009).

In other embodiments, the term “clock gene” can also include genesinvolved in the transmission of signals from clock genes to other genes.For example, in cyanobacteria, genes encoding proteins involved in thetransmission of signals from clock genes include RpaA, RpaB, SasA, andΔCikA, and homologs thereof. For clarity sake, these additional genescan be referred to as signal-transmitting clock genes. In someembodiments, the expression of a target gene can be increased bymodulating the activity of one of these signal-transmitting clock genes.For example, in some embodiments the clock gene is ΔCikA, and expressionof the clock gene is eliminated or suppressed.

Specific polynucleotides/genes useful in the methods and compositions ofthe invention are described herein. However, it should be recognizedthat absolute identity to such genes is not necessary, as substantiallysimilar polynucleotides/genes that perform substantially similarfunctions can also be used in the compositions and methods of thepresent disclosure. For example, changes in a particular gene orpolynucleotide containing a sequence encoding a polypeptide or enzymecan be performed and screened for activity. Typically such changesinclude conservative mutation and silent mutations. Such modified ormutated polynucleotides and polypeptides can be screened for expressionor function of enzymes using methods known in the art. Additionally,homologs of the polynucleotides/genes of the present disclosure aresuitable for use in the compositions and methods disclosed herein.

Due to the inherent degeneracy of the genetic code, polynucleotideswhich encode substantially the same or a functionally equivalentpolypeptide can also be used to clone and express the same polypeptidesor enzymes. As will be understood by those of skill in the art, it canbe advantageous to modify a coding sequence to enhance its expression ina particular host. The genetic code is redundant with 64 possiblecodons, but most organisms typically use a subset of these codons. Thecodons that are utilized most often in a species are called optimalcodons, and those not utilized very often are classified as rare orlow-usage codons.

Those of skill in the art will recognize that, due to the degeneratenature of the genetic code, a variety of DNA compounds differing intheir nucleotide sequences can be used to encode a given polypeptide.The present disclosure includes DNA compounds of any sequence thatencode the amino acid sequences of the polypeptides described herein. Insimilar fashion, a polypeptide can typically tolerate one or more aminoacid substitutions, deletions, and insertions in its amino acid sequencewithout loss or significant loss of a desired activity.

Homologs of genes or proteins are encompassed by the photosyntheticorganisms and methods provided herein. The term “homologs” used withrespect to an original polypeptide or gene of a first family or speciesrefers to distinct enzymes or genes of a second family or species whichare determined by functional, structural or genomic analyses to be apolypeptide or gene of the second family or species which corresponds tothe original polypeptide or gene of the first family or species. Mostoften, homologs will have functional, structural or genomicsimilarities. Techniques are known by which homologs of a gene orpolypeptide can readily be cloned using genetic probes and PCR. Homologscan be identified by reference to various databases and identity ofcloned sequences as homolog can be confirmed using functional assaysand/or by genomic mapping of the genes.

A protein has “homology” or is “homologous” to a second protein if thenucleic acid sequence that encodes the protein has a similar sequence tothe nucleic acid sequence that encodes the second protein.Alternatively, a protein has homology to a second protein if the twoproteins have “similar” amino acid sequences. Thus, the term “homologousproteins” is defined to mean that the two proteins have similar aminoacid sequences.

As used herein, two proteins (or a region of the proteins) aresubstantially homologous when the amino acid sequences have at leastabout 30%, 40%, 50% 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, or 99% identity. Similarly, two polynucleotides(or a region of the polynucleotides) are substantially homologous whenthe nucleic acid sequences have at least about 30%, 40%, 50% 60%, 65%,70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%identity. To determine the percent identity of two amino acid sequences,or of two nucleic acid sequences, the sequences are aligned for optimalcomparison purposes (e.g., gaps can be introduced in one or both of afirst and a second amino acid or nucleic acid sequence for optimalalignment and non-homologous sequences can be disregarded for comparisonpurposes). The amino acid residues or nucleotides at corresponding aminoacid positions or nucleotide positions are then compared. When aposition in the first sequence is occupied by the same amino acidresidue or nucleotide as the corresponding position in the secondsequence, then the molecules are identical at that position (as usedherein amino acid or nucleic acid “identity” is equivalent to amino acidor nucleic acid “homology”). The percent identity between the twosequences is a function of the number of identical positions shared bythe sequences, taking into account the number of gaps, and the length ofeach gap, which need to be introduced for optimal alignment of the twosequences.

The term “increased expression” or “overexpression” as used herein meansany form of expression that is additional to the original wild-typeexpression level. Methods for increasing expression of genes or geneproducts are well documented in the art and include, for example,overexpression driven by appropriate promoters, the use of transcriptionenhancers or translation enhancers. Isolated nucleic acids which serveas promoter or enhancer elements may be introduced in an appropriateposition (typically upstream) of a non-heterologous form of apolynucleotide so as to upregulate expression of a nucleic acid encodingthe polypeptide of interest. For example, endogenous promoters may bealtered in vivo by mutation, deletion, and/or substitution (see U.S.Pat. No. 5,565,350 and International Publication WO9322443), or isolatedpromoters may be introduced into a cell of a photosynthetic organism inthe proper orientation and distance from a gene of the present inventionso as to control the expression of the gene.

Reference herein to “decreased expression” or “reduction or elimination”of expression is taken to mean a decrease in endogenous gene expressionand/or polypeptide levels and/or polypeptide activity relative tocontrol organisms. This reduction or substantial elimination ofexpression may be achieved using routine tools and techniques. Thereduction or substantial elimination is in increasing order ofpreference at least 10%, 20%, 30%, 40% or 50%, 60%, 70%, 80%, 85%, 90%,or 95%, 96%, 97%, 98%, 99% or more reduced compared to that of controlorganisms.

Decreased expression can result from a functional deletion, including amutation, partial or complete deletion, insertion, or other variationmade to a gene sequence or a sequence controlling the transcription of agene sequence, which reduces or inhibits production of the gene product,or renders the gene product non-functional. In some instances afunctional deletion is described as a knockout mutation. Decreasedexpression can also includes amino acid sequence changes by altering thenucleic acid sequence, placing the gene under the control of a lessactive promoter, down-regulation, expressing interfering RNA, ribozymesor antisense sequences that target the gene of interest, or through anyother technique known in the art. In one example, the sensitivity of aparticular enzyme to feedback inhibition or inhibition caused by acomposition that is not a product or a reactant (non-pathway specificfeedback) is lessened such that the enzyme activity is not impacted bythe presence of a compound. In other instances, an enzyme that has beenaltered to be less active can be referred to as attenuated.

A “deletion” is the removal of one or more nucleotides from a nucleicacid molecule or one or more amino acids from a protein, the regions oneither side being joined together.

A “knock-out” is a gene whose level of expression or activity has beenreduced to zero. In some examples, a gene is knocked-out via deletion ofsome or all of its coding sequence. In other examples, a gene isknocked-out via introduction of one or more nucleotides into itsopen-reading frame, which results in translation of a non-sense orotherwise non-functional protein product.

Another method for the reduction or substantial elimination ofexpression of a clock gene is by introducing and expressing in aphotosynthetic organism a genetic construct into which the nucleic acid(in this case a stretch of substantially contiguous nucleotides derivedfrom the gene of interest, or from any nucleic acid capable of encodingan ortholog, paralog or homolog of any one of the protein of interest)is cloned as an inverted repeat (in part or completely), separated by aspacer (non-coding DNA). This results in RNA-mediated silencing of thegene.

In some embodiments, clock gene expression is increased by including apromoter that is operably linked to the clock gene. The term “promoter”refers to a nucleic acid sequence that regulates, either directly orindirectly, the transcription of a corresponding nucleic acid codingsequence to which it is operably linked. The promoter may function aloneto regulate transcription, or, in some cases, may act in concert withone or more other regulatory sequences such as an enhancer, silencer, ortranscription factor to regulate transcription of the transgene. Whenthe promoter is acting in conjunction with other factors such as atranscription factor, it is referred to herein as a promoter system. Thepromoter comprises a DNA regulatory sequence, wherein the regulatorysequence is derived from a gene, which is capable of binding RNApolymerase and initiating transcription of a downstream (3′-direction)coding sequence.

A promoter generally comprises a sequence that functions to position thestart site for RNA synthesis. The best-known example of this is the TATAbox, but in some promoters lacking a TATA box, such as, for example, thepromoter for the mammalian terminal deoxynucleotidyl transferase geneand the promoter for the SV40 late genes, a discrete element overlyingthe start site itself helps to fix the place of initiation. Additionalpromoter elements regulate the frequency of transcriptional initiation.The spacing between promoter elements frequently is flexible, so thatpromoter function is preserved when elements are inverted or movedrelative to one another To bring a coding sequence “under the controlof” a promoter, one positions the 5′ end of the transcription initiationsite of the transcriptional reading frame “downstream” of (i.e., 3′ of)the chosen promoter. The “upstream” promoter stimulates transcription ofthe DNA and promotes expression of the encoded RNA. Alternative ribosomebinding sites, such as the IRES elements (internal ribosome entrysites), can also be used as sites for control of expression.

A promoter may be one naturally associated with a nucleic acid sequence,as may be obtained by isolating the 5′ non-coding sequences locatedupstream of the coding segment and/or exon. Such a promoter can bereferred to as “endogenous.” Alternatively, certain advantages may begained by positioning the coding nucleic acid segment under the controlof a recombinant or heterologous promoter, which refers to a promoterthat is not normally associated with a nucleic acid sequence in itsnatural environment. Such promoters may include promoters of othergenes, and promoters isolated from any virus, or prokaryotic oreukaryotic cell, and promoters not “naturally occurring,” i.e.,containing different elements of different transcriptional regulatoryregions, and/or mutations that alter expression. Furthermore, it iscontemplated the control sequences that direct transcription and/orexpression of sequences within non-nuclear organelles such asmitochondria, chloroplasts, and the like, can be employed as well.

In some embodiments, the promoter is an inducible promoter. In someembodiments, the promoter is a constitutive promoter. As used herein,“inducible promoter” refers to a promoter that drives expression of apolynucleotide to which it is operably linked upon cellular perceptionof a stimulus. Likewise, inducible promoters can terminate expression ofa polynucleotide to which it is operably linked upon removal of astimulus. An example of an inducible promoter in the present disclosureis the isopropyl-β-D-thiogalactoside (IPTG) inducible promoter, in whichthis promoter drives expression of a polynucleotide to which it isoperably linked upon perception of IPTG, an exogenous chemical. Anyappropriate inducible promoter that has use in the compositions andmethods of the present disclosure may be used accordingly. One of skillin the art will recognize that many characterized inducible promotersexist and can be used according to the compositions and methodsdisclosed herein. Constitutive promoters, on the other hand, are thosepromoters that are substantially insensitive to regulation by externalstimuli and promote expression of a given polynucleotide in anessentially constant manner.

Increased Expression of a Target Gene

The present invention includes modulating the expression of a clock geneto increase expression of a target gene. A wide variety of target genescan be used within the scope of the present invention. In someembodiments, the target gene is an endogenous gene, while in otherembodiments the target gene is a heterologous gene. Preferably thetarget gene is a gene capable of expressing a polypeptide. When thetarget gene is a heterologous gene, the photosynthetic organism will be,by definition, a transgenic photosynthetic organism.

In some embodiments, the target gene is a gene influencing theexpression of a biofuel product or biofuel precursor. A target geneinfluencing the expression of a biofuel product or biofuel precursor canbe either an endogenous gene or a heterologous gene. A wide variety ofphotosynthetic organisms naturally express biofuel products orprecursors as a part of their regular metabolism, through the expressionof endogenous genes. However, in other cases, photosynthetic organismsare transformed through the incorporation of heterologous genes. See forexample US 2014/0186877, which describes engineered microorganismsincluding an alpha-olefin-associated enzyme is incorporated intocyanobacteria to increase 1-alkene production.

A “biofuel” as used herein is any fuel that derives from a biologicalsource. A “fuel” refers to one or more hydrocarbons, one or morealcohols, one or more fatty esters or a mixture thereof. Preferably,liquid hydrocarbons are used.

“Biofuel precursors,” as used herein, refer to lipids and oils producedby algae that are organic compounds suitable for use in preparing abiofuel. While the lipids and oils will typically require additionalprocessing before being used as biofuels, in some instances they may beused directly without additional processing. Lipids, as defined herein,include naturally occurring fats, waxes, sterols, monoglycerides,diglycerides, triglycerides, and phospholipids. The preferred lipids arefatty acid lipids found in triacylglycerides. Free fatty acids aresynthesized in algae through a biochemical process involving variousenzymes such as trans-enoyl-acyl carrier protein (ACP),3-hydroxyacyl-ACP. 3-ketoacyl-ACP, and acyl-ACP. Examples of free fattyacids include fatty acids having a chain length from 14 to 20, withvarying degrees of unsaturation. A variety of lipid-derived compoundscan also be useful as biofuel and may be extracted from oleaginousalgae. These include isoprenoids, straight chain alkanes (with short(3-7 carbon) and medium (8 to 12 carbon) chain lengths), and long andshort chain alcohols, such short chain alcohols including ethanol,butanol, and isopropanol.

While biofuel is an example of a product whose expression can beincreased as a result of increased expression of either endogenous orheterologous gene expression, in some embodiments, the invention isdirected solely to increased expression of an endogenous gene. Examplesof endogenous genes that can be readily influenced by manipulating thecircadian clock of a photosynthetic organism include “ClassI”/“subjective dusk” genes, which activate at down and risk throughoutthe day to peak expression at dusk, and “Class II/“subjective dawn”genes, which activate at night and peak at dawn. The inventors haveidentified a large number of genes that respond to the circadian clock,and have shown that KaiC overexpression represses the predominant ClassI dusk genes, while up-regulating Class II dawn genes, while KaiAoverexpression acts in the opposite manner, in a “Yin-Yang”interdependency.

In other embodiments, the invention is directed solely to increasedexpression of a heterologous gene. Preferably, the heterologous gene isa gene capable of expressing a protein, and in particular a proteinhaving practical value, such as a medically or industrially usefulprotein. Examples of proteins that have been recombinantly expressedinclude chymosin, human insulin, human growth hormone, blood clottingfactor VIII, hepatitis B vaccine, and hydrogenase. In particular, workby the inventors have demonstrated manipulating the circadian clock toincrease expression of hydrogenase and pro-insulin.

Photosynthetic Organisms Having a Modified Circadian Cycle

Another aspect of the invention provides a photosynthetic organismhaving a modified circadian cycle. The circadian cycle is modified bytransforming a photosynthetic organism to include an expression controlsequence that modulates the expression of a clock gene to increaseexpression of a target gene. The presence of a circadian cycle appearsto be nearly universal, occurring not only in all plants thus farexamined, but also in insects and microbes.

In some embodiments, the photosynthetic organism is a plant. Circadianrhythms control many aspects of plant metabolism, physiology anddevelopment. Plants make use of environmental signals such as the dailylight-dark cycle or regular temperature variations to maintain abiological time-keeping mechanism. This mechanism, known as thecircadian clock, is commonly represented as a so-called oscillator thatconsists of a set of proteins which interact in a complex pattern ofpositive and negative transcriptional feedback loops, for a review seeMcClung, C. R., Plant Cell 18, 792-803, 2006. The oscillator iscalibrated by external signals (such as light, perceived by phytochromesand cryptochromes) which are transmitted via the “input pathways” to theoscillator. The oscillator on its turn controls a number of pathways(the “output pathways”) which regulate physiological processes that areinfluenced by the daily environmental changes. An overview is given inBarak et al., Trends in Plant Science 5, 517-522, 2000, and include forexample induction of flowering, opening of petals, opening or closure ofstomata, growth of the hypocotyl, movement of cotyledons and leaves,movement of chloraplasts, expression of genes associated withphotosynthesis and related biochemical and physiological processes,cytoplasmic calcium concentrations, and the phosphorylation status ofproteins like phosphoenol pyruvate carboxylase. For example, modulatingexpression of a nucleic acid encoding a HUB1 (HistoneMonoubiquitination 1) has been shown to alter various growthcharacteristics in a plant. See U.S. Pat. No. 9,074,006.

Expression of the circadian clock proteins may be modified in a widerange of higher plants to confer altered circadian clock and/orphotoperiodism function, including monocotyledonous and dicotyledenousplants. These include, but are not limited to, Arabidopsis, Cardamine,cotton, tobacco, maize, wheat, rice, barley, soybean, beans in general,rape/canola, alfalfa, flax, sunflower, safflower, brassica, cotton,flax, peanut, clover; vegetables such as lettuce, tomato, cucurbits,cassava, potato, carrot, radish, pea, lentils, cabbage, cauliflower,broccoli, Brussels sprouts, peppers; tree fruits such as citrus, apples,pears, peaches, apricots, walnuts; other trees including poplar, oak,maple, pine, spruce and other conifers; and flowers or other ornamentalplants such as carnations, roses, petunias, orchids, impatiens, pansies,lilies, snapdragons, geraniums, and so forth.

In some embodiments, the photosynthetic organism is algae. A widevariety of algae are suitable for genetic modification. Among these aredinoflagellates (e.g., Ampidinium, Symbidinium), diatoms (e.g.,Phaeodactylum, Cyclotella, Navicula, Cylindrotheca, Thalassiosira),green algae (e.g. Chlamydomonas, Chlorella, Haematococcus, Dunaliella,Ostreococcus, Coccomyxa), red algae (e.g., Porphyridium, Kappaphycus,Galdieria), macroalgae (e.g., Ulva), and bluegreen algae (e.g.,Synechocystis, Synechococcus, Anabaena, Nostoc). The methods andprotocols have been described in the literature and are incorporatedhere by reference (Leon & Fernandez, Advances in Experimental Medicineand Biology, Ch. 1, 616 1-129 (2007)); Packer & Glazer, Meth Enzymol167, p. 1-910 (1988); Bryant, The molecular biology of Cyanobacteria.Advances in Photosynthesis, Kluwer Academic Publishers. 880 pp (1994)).

For example, the algae that are genetically modified can be selectedfrom the group consisting of cyanophyta, rhodophyta, heterokontophyta,haptophyta, cryptophyta, dinophyta, euglenophyta, and chlorophyta. Thegenetically modified alga can also be a species selected from the groupconsisting of Chlamydomonas sp., Chlorella sp., Nannochloropsis sp.,Synechocystis sp., Synechococcus, Anabaena sp., Cyclotella,Phaeodactylum sp., Crypthicodineum sp., Ulkenia, Schizochytridum sp.,Haematococcus sp., Arthrospira (Spirulina) sp., Galdieria sp.,Ostreococcus sp., Coccomyxa sp. and Dunaliella sp.

Methods for the transformation of various types of algae are known tothose skilled in the art. See for example Radakovits et al., EukaryoticCell, 9, 486-501 (2010), which is incorporated herein by reference. Thetransformation of the chloroplast genome was the earliest method and iswell documented in the literature (Kindle et al., Proc Natl Acad Sci.,88, p. 1721-1725 (1991)). A variety of methods have been used totransfer DNA into microalgal cells, including agitation in the presenceof glass beads or silicon carbide whiskers, electroporation, biolisticmicroparticle bombardment, and Agrobacterium tumefaciens-mediated genetransfer. A preferred method of transformation for the present inventionis biolistic microparticle bombardment, carried out with a devicereferred to as a “gene gun.”

In other embodiments, the photosynthetic organism is a photoautotrophicor photoheterotrophic bacteria. Photoautotrophic and photoherotrophicbacteria are bacteria that derive at least part of their energy fromphotosynthesis. Photoautotrophic bacteria derive their energyexclusively from light, whereas photoheterotrophic bacteria areorganisms that use light for energy, but cannot use carbon dioxide astheir sole carbon source, and therefore use organic compounds from theenvironment to satisfy their carbon requirements.

Because of their increased dependence on solar energy, and theassociated need for circadian regulation, photoautotrophic bacteria areof particular interest for use in the present invention.Photoautotrophic bacteria are typically Gram-negative rods which obtaintheir energy from sunlight through the processes of photosynthesis. Inthis process, sunlight energy is used in the synthesis of carbohydrates,which in recombinant photoautotrophs can be further used asintermediates in the synthesis of biofuels. In other embodiment, thephotoautotrophs serve as a source of carbohydrates for use bynonphotosynthetic microorganism (e.g., recombinant E. coli) to producebiofuels by a metabolically engineered microorganism. Certainphotoautotrophs called anoxygenic photoautotrophs grow only underanaerobic conditions and neither use water as a source of hydrogen norproduce oxygen from photosynthesis. Other photoautotrophic bacteria areoxygenic photoautotrophs. These bacteria are typically cyanobacteria.They use chlorophyll pigments and photosynthesis in photosyntheticprocesses resembling those in algae and complex plants. During theprocess, they use water as a source of hydrogen and produce oxygen as aproduct of photosynthesis (see, e.g. US 2011/0250060).

In some embodiments, the present invention provides cyanobacteria thatcontain an expression control sequence for manipulating the circadianclock. Cyanobacteria include various types of bacterial rods and cocci,as well as certain filamentous forms. The cells contain thylakoids,which are cytoplasmic, platelike membranes containing chlorophyll. Insome embodiments, the cyanobacteria are a Synechococcus sp. In someembodiments, the Synechococcus sp. is Synechococcus elongatus. In someembodiments, the Synechococcus elongatus is Synechococcus elongatusPCC7942. One of skill in the art will recognize that other cyanobacteriacan be used according to the present disclosure. Examples of otherexemplary cyanobacteria include marine cyanobacteria such asSynechococcus sp. WH8102, thermostable cyanobacteria such asThermosynechococcus elongatus BP-1, photoheterotrophic cyanobacteriasuch as Synechocystis sp. PCC6803 and filamentous cyanobacteria such asNostoc punctiforme.

The following examples have been included to more clearly describeparticular embodiments of the invention. However, there are a widevariety of other embodiments within the scope of the present invention,which should not be limited to the particular examples provided herein.

EXAMPLES Example 1: Circadian Yin-Yang Regulation and its Manipulationto Globally Reprogram Gene Expression

The cyanobacterial circadian program exerts genome-wide control of geneexpression. KaiC undergoes rhythms of phosphorylation that are regulatedby interactions with KaiA and KaiB. The phosphorylation status of KaiCis thought to mediate global transcription via output factors SasA,CikA, LabA, RpaA, and RpaB. Overexpression of kaiC has been reported toglobally repress gene expression.

The inventors show that the positive circadian component KaiAupregulates “subjective dusk” genes and its overexpression de-activatesrhythmic gene expression without significantly affecting growth rates inconstant light. The global patterns of expression that are regulated byKaiA versus KaiC were analyzed, and it was found, in contrast to theprevious report of KaiC repression, that there is a “Yin-Yang”regulation of gene expression whereby kaiA overexpression activates“dusk genes” and represses “dawn genes,” whereas kaiC overexpressioncomplementarily activates “dawn genes” and represses “dusk genes.”Moreover, continuous induction of kaiA latched KaiABC-regulated geneexpression to provide constitutively increased transcript levels ofdiverse endogenous and heterologous genes that are expressed in thepredominant “subjective dusk” phase. In addition to analyzing KaiAregulation of endogenous gene expression, these insights were applied tothe expression of heterologous proteins whose products are of potentialvalue, namely human proinsulin, foreign luciferase, and exogenoushydrogenase.

Both KaiC and KaiA complementarily contribute to the regulation ofcircadian gene expression via Yin-Yang switching. Circadian patterns canbe reprogrammed by overexpression of kaiA or kaiC to constitutivelyenhance gene expression, and this reprogramming can improve 24/7production of heterologous proteins that are useful as pharmaceuticalsor biofuels.

Experimental Procedures

Promoter/reporter constructs. Vibrio harveyi luciferase encoded by luxAand luxB (luxAB) genes was used as a luminescence reporter of expressionactivities from various promoters from either Escherichia coli orSynechococcus elongatus PCC 7942. The kaiAp::luxAB expression cassettewas made by fusing a 0.24 kb upstream fragment (produced from Dra II EagI cleavage) of the kaiA gene to luxAB and then inserted into the EcoRVsite of a neutral site II vector pAM1579 that includes a kanamycinselection marker (Km^(r)). A 260-bp PCR fragment covering the 5′upstream portion of the E. coli σ70 binding site gene conII and a 300-bpPCR fragment containing the upstream region of the purine biosynthesispathway gene purF were respectively cloned into the Not I/BamH I site ofa promoterless luxAB vector pAM1414 to give rise to conIIp::luxAB andpurFp::luxAB reporters in NS I. A 2.44-kb DNA fragment harboring luxABcoding regions was inserted into the Nde I site of the neutral site Iexpression vector pTrc-NS I with a spectinomycin resistance (Spec^(r))marker to make the trcp::luxAB reporter construct, in which theexpression of luxAB genes was under the control of an IPTG (isopropylβ-D-1-thiogalactopyranoside)-inducible trc promoter that is regulated bythe repressor lacI^(q). (FIG. 9A). Construction of other reporters wasdescribed previously, including kaiBCp::luxAB in NS I (Xu et al., EMBOJ. 22, 2117-2126 (2003)), fisp::luxAB (chloramphenicol resistance, Cm′)in NS I (Min et al., J. Biol. Rhythm. 19, 103-112 (2004)), ftsZp::luxAB(Km^(r)) in NS II (Mori, T., and Johnson, C. H., J. Bacteriol. 183,2439-2444 (2001)), and psbAIp::luxAB (Spec^(r)) in NS I (Kondo et al.,Proc. Natl. Acad. Sci. USA 90, 5672-5676 (1993).

Generation of kaiA-overexpressing strains. To “reprogram” the circadianregulation of global gene expression in different reporter backgrounds,three versions of IPTG-derepressible kaiA-expressing constructs wereused. The first one used the open reading frame (positions+1˜825) ofwild-type kaiA (GTG translation start codon) with its 5′- and3′-flanking sequences (from −27 to −1 and from +826 to +905) cloned intothe downstream EcoR I/Xba I site of the trc promoter on pTrc-NS I tomake the construct trcp::kaiA in NS I with a Spec^(r) selection marker.The second version was a trcp::kaiA fusion into NS II with a Km^(r)selection marker. Kutsuna et al., J. Bacteriol. 189, 7690-7696 (2007).The third version was the trc promoter-driven kaiA coding region with anATG translation start codon [trcp::{ATG}kaiA] located in NS II with aKm^(r) marker. These versions of kaiA-expressing constructs wereintroduced into appropriate reporter strains or foreign gene-expressingstrains via double homologous recombination. For induction of thetrcp-driven (WT)kaiA or {ATG}kaiA expression, the indicatedconcentration of IPTG or an equivalent volume of water (as control) wasadministered to the liquid cultures or under the agar medium asspecified. For the kaiA-overexpressing strains used in this study, theywere all (WT)kaiA versions unless {ATG}kaiA is specifically indicated.

Foreign gene-expressing strains. Generation of the cyanobacterial RC41strain that expresses the gene cluster encoding A. macleodii DeepEcotype [NiFe] hydrogenase HynSL and other 11 surrounding accessoryproteins in NS I was described previously (Weyman et al., PLoS ONE 6,e20126 (2011)), in which the endogenous cyanobacterial hoxYH genesencoding the bidirectional [NiFe] hydrogenase (HoxYH) were deleted. Tomake a strain expressing a fusion protein between glutathioneS-transferase (GST) and human proinsulin (HPI), the HPI coding sequencefrom a human cDNA clone BC005255 (OriGene, Rockville, Md.) was fused tothe C-terminal EcoR I site of the GST tag from the vector pGEX-6P-1 (GEHealthcare Bio-Sciences Corp., Piscataway, N.J.). A PCR fragmentcontaining the GST-HPI fusion with a linker was cloned downstream of theconII promoter. After confirmation of the construct with a Spec^(r)marker and by DNA sequencing, the conIIp::GST-HPI expression cassettewas introduced into the NS I site.

Growth conditions and luminescence measurements. The cyanobacterium S.elongatus PCC 7942 was grown in modified BG11 liquid media with airbubbling or on BG11 agar plates supplemented with appropriateantibiotics (spectinomycin, 40 μg/ml; kanamycin, 10 μg/ml; erythromycin,5 μg/ml; chloramphenicol, 7.5 μg/ml) at 30° C. under continuouscool-white illumination (LL) (50 μE/m² s). Bustos et al., J. Bacteriol.173, 7525-7533 (1991). Before the cells were released into LL, 1˜2cycles of the 12 hr/12 hr light/dark (LD) were given to synchronize thecultured cells. In vivo luminescence assays in cyanobacteria wereperformed as described previously for liquid cultures (3 vials eachsample) or for colonies on agar (12 colonies each sample). Forluminescence assays in E. coli, 20 μl of 1% n-decanal was mixed with 0.5ml of cells at OD₆₀₀=0.5, and the total luciferase activities wereimmediately measured with FB12 Luminometer (Zylux Corporation, Germany).Growth rates of cyanobacterial strains were determined in atemperature-controlled shaking water bath with shaking at 100 rpm andwith air bubbling into the cultures. Initial cultures were grown inliquid BG-11 medium at 30° C. under constant illumination (50 μE/m² s)in a shaking water bath at 100 rpm and with air bubbling into thecultures. Cell densities were monitored by measuring the optical densityat 750 nm (OD₇₅₀). When cell densities reached OD₇₅₀˜0.8, cultures werediluted to OD₇₅₀˜0.005, and grown in LL in water baths set to 30° C.with shaking (100 rpm) and air bubbling in presence or absence of IPTG.Cell densities were determined at OD₇₅₀ over a time course as indicated.When OD₇₅₀ values of cell cultures exceed 0.9, the OD measurement is notlinear with cell density. Therefore, for samples with an OD₇₅₀ that waslarger than 0.9, the samples were diluted to an OD₇₅₀ that was withinthe linear range before OD determination (and the plotted OD value thenis corrected for the dilution). Two independent experiments wereperformed for each strain, and the growth curves were plotted as averageOD₇₅₀ values over time in LL. For microarray and Northern blottinganalyses, Synechococcus cells were grown in BG11 media in a continuousculture system (optical density of around 0.25 at 730 nm) at 30° C. and40 μE/m² s. To synchronize the circadian clock, the culture wasacclimated to 2 LD cycles and then transferred to LL in the presence orabsence of 1 mM IPTG applied at LL24.

Microarray analysis. Total RNA was purified with the modified acid-hotphenol method. Iwasaki et al., Cell 101, 223-233 (2000). From total RNAsamples, 1.5 μg of cDNA was prepared with a SuperScript III reversetranscriptase (Invitrogen) using random hexamers as primers(Invitrogen), partially fragmented with DNasel (Takara) and biotylatedby using an ENZO BioArray Terminal Labeling kit (ENZO Life Sciences).The labeled cDNAs were hybridized to the GeneChip arrays. The arrayswere hybridized, washed, and stained by using standard Affymetrixprokaryotic GeneChip reagents and protocols. Affymetrix Gene Chipsoftware was used to determine the average difference between matchedmismatched oligonucleotide probes for each probe set. For betterestimation of relative expression levels among different genes, westandardized each cDNA-derived signal with the corresponding genomicDNA-derived signal. We also performed hybridization of the Synechococcusoligonucleotide arrays with biotin-labeled DNasel-fragmented genomicDNA.

The genomic DNA-derived signals varied within a range of 10-fold,whereas the RNA-derived signals (wild-type RNA samples collected at LL12 as example) varied within a range of 10³-fold. The signals forgenomic DNA were within a linear range. Genomic DNA signals were scaledso that their average level was 1. Each RNA signal was then divided bythe corresponding scaled genomic DNA signal. Values of RNA signals givenhereafter indicate these genomic-DNA-normalized values. Ito et al.,Proc. Natl. Acad. Sci. USA 106, 14168-14173 (2009). The raw data havebeen deposited in the National Center for Biotechnology Information'sGene Expression Omnibus database with an accession number GSE47015).Additionally, global normalization was applied to the RNA signalprofiles under LL conditions so that the averages of the expressionlevels for all ORFs within a microarray were equal across arrays.

For normalization of microarray profiles presented in FIG. 1A, theaverages and the standard deviations of the time-course profiles (LL30-48, -IPTG) for each gene were initially calculated, and then theaverage values were subtracted from the signal at each indicated time,so that the time-course average level is 0. Finally, the edited signalvalues were divided by the standard deviation to normalize the resultingSD to 1.

Northern blots. Cells were harvested and immediately stored at −80° C.until RNA extraction. RNA was extracted from each sample as describedabove, and then subjected to electrophoresis, blotted onto nylonmembranes, and hybridized with digoxigenin-labeld probes as describedpreviously. Ishiura et al., Science 281, 1519-1523 (1998).

Quantitative real-time PCR (qRT-PCR). Total RNA was extracted by the hotphenol method with some modifications. Mohamed, A., and Jansson, C.Plant Mol. Biol. 13, 693-700 (1989) The cells collected from 30 mlcultures were treated with 1 ml Trizol, and incubated in a 65° C. waterbath for 5 min. 0.2 ml chloroform was added per ml of Trizol andincubated in the 65° C. water bath for another 15 min, shaking from timeto time to facilitate lysis. The subsequent phase extraction was doneaccording to the Trizol extraction method. The extracted RNA was treatedwith the TURBO DNA free TM kit (Ambion) twice according to theinstruction manual. About 1000 ng RNA was reverse-transcribed using theAgilent AffinityScript qPCR cDNA synthesis kit. The kaiA and kaiBCtranscript levels were determined by quantitative RT-PCR. Thehousekeeping gene rnpB was chosen as an internal control gene to measurethe relative levels of mRNA of target genes in vivo. Primer sequencesare as follows: rnpB, f5′-GAAACATACCGCCGATGG-3′ (SEQ ID NO: 6) andr5′-GTTGCTGGTGCGCTCTTAC-3′ (SEQ ID NO: 7); kaiA,f5′-TCGCGACAGTGAGGATCCCGA-3′ (SEQ ID NO: 8) andr5′-GTCTCGACCGGGGCTAAGCG-3′ (SEQ ID NO: 9); kaiBC,f5′-GGAATATCCGTTCACGATTACG-3′ (SEQ ID NO: 10) andr5′-GACGATCGCTGCGTAAGG-3′ (SEQ ID NO: 11). Primer efficiency wasdetermined using a standard curve for all the primers listed. AllqRT-PCRs were carried out using an Applied Biosystems 73000 Real-timeRCR system with SYBR green as fluorescent dye, and the specificity ofeach primer pair was tested by a melting curve analysis. Threeexperimental replications were performed and the raw data were processedusing System 7300 Sequence Detection Software.

Immunoblotting for protein abundance. Cyanobacterial cells wereharvested at the indicated time points. Total proteins were extracted aspreviously described (Xu et al., EMBO J. 19, 3349-3357 (2000)) andseparated by SDS-polyacrylamide gel electrophoresis (PAGE) (15% forKaiA, KaiB, and GST-HPI; 10% for KaiC, Lux, and HyaB assays) andtransferred onto nitrocellulose membranes. Gels were either stained withCoomassie Brilliant Blue (CBB) or transferred to nitrocellulose forimmunoblotting using polyclonal rabbit antisera (raised against KaiA orKaiB or Thiocapsa roseopersicina HynL), monoclonal mouse antisera(raised against KaiC), polyclonal rabbit antisera against bacterialluciferase, or an affinity chromatography-purified GST epitope tagantibody (originally from polyclonal rabbit antisera, Novus, Littleton,Colo.). The immunoblots were analyzed with NIH Image J software.

Hydrogenase activity assays. In vitro hydrogen evolution assays wereperformed using cyanobacterial cell extracts, as described previously(Maroti et al., Appl. Environ. Microbiol. 75, 5821-5830 (2009)) with thefollowing modifications. Cells (500 ml) were grown with constant airsparging and stirring at 28° C. under cool white fluorescence (30 μE m⁻²s⁻¹). After indicated treatments, cells were centrifuged, resuspended in1 ml sonication buffer (10 mM Tris-HCl, pH 7, 0.5 mM EDTA, 1 mM DTT),and sonicated under aerobic conditions twice for 2 minutes each on icebefore being used for assays. The cell debris were removed bycentrifugation, and the supernatants were used for hydrogenase activityassays. Hydrogenase assays were performed in 13.5 mL serum vialscontaining a total reaction volume of 2 mL consisting of 25 mM potassiumphosphate, pH 7.0, 2 mM methyl viologen, and cell extract (approximately20 μg total protein). The assay vials were capped with rubber septa andsparged with argon gas to remove oxygen, and 100 μl of 2M sodiumdithionite pH 7.0 was added to begin the reaction. Reactions wereincubated at 30° C., and at various time points 100 μl of headspacegases including hydrogen were analyzed by gas chromatography (CP-3800,Varian) using a Fused Silica Molsieve 5A column (CP7537, Varian).

Student's t-test and R-squared were performed for statistical analyses.

Results KaiA-OX Enhances Expression of Subjective Dusk Genes: MicroarrayAnalyses

In vivo overexpression of kaiC has been claimed to globally repress geneexpression in S. elongatus (Nakahira et al., Proc. Natl. Acad. Sci. USA101, 881-885 (2004)), but the converse manipulation of pervasivelyenhancing gene expression by manipulation of the clock has not beenstudied. Since the KaiABC-based oscillator globally regulates geneexpression in cyanobacteria and kaiA-OX enhances the expression of thekaiBC promoter (Ishiura et al., Science 281, 1519-1523 (1998)), wereasoned that KaiA could be enlisted to act as a positive regulator toenhance expression on a genomic scale. Using a luciferase reporter ofthe expression of the Class I photosynthetic gene psbAl (psbAIp::luxAB),we found that the response of the psbAl promoter to overexpression ofkaiA (kaiA-OX) is both acute and sensitive (See FIG. 1A-1C). When kaiAexpression was stimulated with the inducer isopropylβ-D-1-thiogalactopyranoside (IPTG), psbAIp::luxAB expression quicklyincreased to a high level that was essentially arrhythmic (FIG. 1B), andthis response to kaiA-OX was dependent on IPTG dose; concentrations ofIPTG as low as 15-20 μM eliminated the clock-controlled luminescencerhythm (FIG. 1C). The addition of IPTG to cells that do not harbor anIPTG-derepressible promoter (i.e., trcp) does not elicit any changes ingene expression. Moreover, overexpression of kaiA had no marked effecton the growth rates among different reporter strains in constant light,aka LL (FIG. 1D).

To evaluate KaiA's genome-wide regulation, we performed microarrayassays in the kaiA-overexpressing strains with or without IPTG induction(FIG. 2A). The expression profile of each clock-controlled gene inkaiA-OX cells with IPTG induction in constant light (LL) from 30 to 48 hwas compared with that in the absence of IPTG (LL30-48) (FIG. 2A). Inresponse to kaiA-OX, about 20% of the genes were up-regulated and about12% were down-regulated, with the remaining ˜68% of genes not clearlyaffected by kaiA-OX. In comparison with the genes that are repressed vs.enhanced by overexpression of kaiC (kaiC-OX), there is a clear trendthat kaiA-OX and kaiC-OX have opposite effects for most genes (FIG. 2B;FIGS. 3A and 3B). Among 800 cycling genes revealed by microarrays,kaiA-OX mostly up-regulates “subjective dusk” genes (expression mostlyin the daytime, with peak expression at Circadian Time 12 {CT12}≈36 h inLL, aka Class I genes) and down-regulates “subjective dawn” genes (peakexpression at CTO≈24 & 48 h in LL, aka Class II genes, FIG. 2C-2E),whereas kaiC-OX was shown to repress dusk genes and activate dawn genes.Ito et al., Proc. Natl. Acad. Sci. USA 106, 14168-14173 (2009).

Although there may be some positional effects of these opposingregulatory patterns based on rhythmic changes in chromosomal topology,there is not an obvious clustering pattern along the chromosome of thegenes that are up-regulated vs. down-regulated by kaiA-OX (FIG. 3C; FIG.4). On the other hand, there is an obvious correlation of genes alongthe chromosome that are up-regulated by kaiA-OX with those that areinversely down-regulated by kaiC-OX, and vice-versa (FIG. 4), asconfirmed by the statistically significant regression shown in FIG. 2B(R²=0.683). Therefore, kaiA-OX vs. kaiC-OX complementarily regulatecircadian expression patterns. As will be shown below, continuousoverexpression of kaiA locks the expression of these output genes atconstitutively high or low levels and arrests rhythmic expression by theconstitutive hyperphosphorylation of KaiC. Iwasaki et al., Proc. Natl.Acad. Sci. USA 99, 15788-15793 (2002).

Effect of kaiA-OX on Gene Expression at “Neutral Sites” UsingLuminescence Reporters

To monitor in real-time the effect of KaiA on promoter activities, weexamined luminescence reporters driven by the promoters of diverse S.elongatus genes, including the central clock genes (kaiA and kaiBC), thephotosynthesis gene psbAl, the purine biosynthesis pathway gene purF,and the cell division gene ftsZ. These genes exemplify both expressionpatterns: kaiAp, kaiBCp, psbAIp, and ftsZp are Class I promoters, whilepurFp is a Class II promoter. We also examined heterologous E. colipromoters that are recognized by the transcriptional apparatus of S.elongatus, such as those from the fis factor for site-specific DNAinversion (a marker of local DNA topology (Gille et al., Nucleic AcidsRes. 19, 4167-4172 (1991)), an IPTG-derepressible heterologous promotertrc (Xu et al., EMBO J. 22, 2117-2126 (2003)), and the σ70 binding sitegene conII (Elledge, Proc. Natl. Acad. Sci. USA 86, 3689-3693 (1989)),all of which are expressed in the Class I (dusk) phase in S. elongatus(FIG. 5B). Although all of these reporters were expressed in both E.coli and S. elongatus, their expression levels were quite differentbetween these two bacteria. While reporters driven by cyanobacterialpromoters express at much lower levels in E. coli than those from E.coli (a phenomenon that is particularly noticeable in the case of thepsbAl promoter; FIG. 5A), in S. elongatus the E. coli reportersexhibited both the strongest (e.g. conIIp::luxAB) and the weakestexpression (e.g. fisp::luxAB; FIG. 5B). Nevertheless, all of thereporters—independent of the source of the promoter—were rhythmic incyanobacteria (FIG. 5B), a phenomenon that is likely due to circadiancontrol over chromosomal topology in S. elongatus that modulatespromoter activity globally. Woelfle et al., Proc. Natl. Acad. Sci. USA104, 18819-18824 (2007). We then integrated an IPTG-inducible expressioncassette of wild-type kaiA with a 5′-untranslated sequence (trcp::kaiA)into either neutral site I or neutral site II of these reporter strainsto examine the impact of kaiA-OX on the activity of these variouspromoters. Overexpression of kaiA constantly enhanced the promoteractivities of the central clock genes (kaiAp and kaiBCp) when IPTG wasapplied to cells at either the beginning of LL treatment (LL0) or 48 hlater (LL48), whereas kaiBC-OX repressed kaiBCp activity (FIG. 6A; FIGS.7A and 7B).

Moreover, kaiA-OX increased the levels of kaiBC and luxAB transcriptswhen IPTG was added at LL24 (FIG. 6B; FIGS. 7C and 7D). Increased KaiAalso enhanced the abundance of the KaiB and KaiC proteins, and promotedthe hyperphosphorylation of KaiC (FIG. 6C), which is consistent withKaiA's ability to stimulate KaiC phosphorylation in vitro and in vivo,and inhibit dephosphorylation. To obtain even stronger production ofKaiA, in some of our experiments we used an IPTG-derepressibletrcp::kaiA fusion gene with an ATG start codon, i.e. trcp::{ATG}kaiA(rather than the aforementioned construct with a GTG start codon) (FIGS.7E and 7F). In contrast to the consequences of kaiA-OX, kaiC-OX floodsthe system with newly synthesized KaiC, which reduces the overallphosphorylation status of the KaiC pool. Therefore, kaiA-OX and kaiC-OXhave complementary effects on the status of KaiC phosphorylation andtherefore mimic opposite points of the endogenous oscillation of KaiCphosphorylation that are 180° out of phase (see FIG. 12A).

An indicator of the global, non-discriminatory control of the S.elongatus genome by the KaiABC-based clock is whether heterologouspromoters/genes can be controlled in a similar fashion to endogenouspromoters/genes. To determine if kaiA-OX can enhance expression offoreign gene promoters, we tested strains expressing luxAB under thecontrol of conIIp—a strong promoter that is “constitutively” expressedin E. coli. Luminescence activities controlled by conIIp exhibited highlevels of rhythmic expression in S. elongatus, and kaiA-OX furtherenhanced this strong promoter's activity up to ˜3.5 fold higher thanthat of controls without kaiA induction (FIGS. 6D & 6E). This kaiA-OXmediated enhancement of luminescence activity under the control ofconIIp appears to occur by boosting the trough levels of theconIIp::luxAB expression profile to be at or above the peak levels (FIG.6D). KaiA also positively regulates a usefully inducible,non-cyanobacterial promoter, trcp. KaiA-mediated enhancement ofluminescence expression is particularly dramatic in a S. elongatusstrain co-expressing both IPTG-inducible constructs (trcp::luxABreporter and trcp::kaiA) (FIG. 9A). In the absence of IPTG induction,the artificial promoter trc could drive circadian luminescenceoscillations at low levels in both the reporter strain (trcp::luxAB) andthe reporter/kaiA-coexpressing strain (trcp::luxAB+trcp::kaiA; FIG. 6F;FIG. 9B). In the presence of IPTG, overall promoter activity wasincreased in the trcp::luxAB reporter strain but the pattern remainedrhythmic (FIG. 6F), whereas in the strain co-expressing the trcp::luxABreporter and trcp::kaiA, kaiA overexpression further stimulated theactivity of the strong trc promoter but the rhythmic pattern was lost(FIGS. 6F & 6G). Therefore, kaiA-OX not only enhances the expression ofdiverse cyanobacterial “subjective dusk” Class I genes in situ (FIG. 2),it also stimulates the activity of cyanobacterial kai promoters and ofthe strong E. coli promoters conIIp and the IPTG-depressible promotertrcp when placed into neutral sites NSI or NSII (FIG. 6).

Enhancing Expression of Endogenous Hydrogenase Genes by kaiA-OX

The quest to understand the role of KaiA in regulating KaiCphosphorylation status and therefore gene activity led to therecognition that expression of subjective dusk genes (the predominantClass I genes) could be constitutively enhanced by this rewiring of thecircadian circuitry. Thereby, enhanced production of useful bioproducts,such as biofuel compounds encoded by foreign and/or endogenous genes,could be accomplished by kaiA-OX. Hydrogen (H₂) is an attractivecarbon-free energy storage molecule, and production of H₂ usingphotosynthetic cyanobacteria could provide an alternative to fossilfuels by using solar energy to convert H₂O into hydrogen. Hydrogenasescatalyze the reversible reduction of protons to H₂ and can be dividedinto three phylogenetically-distinct categories that correlate with themetal composition of the active site: [FeFe], [NiFe], and[Fe]-cluster-free hydrogenases. S. elongatus has one native [NiFe]hydrogenase. Interestingly, our microarray analysis revealed thatkaiA-OX promoted mRNA profiles of all NAD-reducing hydrogenase subunits(FIG. 8A). Therefore, we first examined the impact of kaiA-OX(trcp::{ATG}kaiA) upon the expression of endogenous [NiFe] hydrogenasein S. elongatus. As shown in FIG. 8B, endogenous [NiFe] hydrogenaseactivities were enhanced in the kaiA-OX strain in constant light evenwithout IPTG induction due to “leaky” expression of KaiA in thetrcp::{ATG}kaiA strain. Mild induction of KaiA with 20 μM of IPTGfurther boosted hydrogenase activity. Overexpression of KaiA also causedconsistently high levels of hydrogenase activity in a LL time courseexperiment in the kaiA-OX strain (+20 μM IPTG) relative to wild-typestrain (FIG. 8C).

kaiA-OX-Enhanced Production of Foreign Proteins in LD, LL, and DD

The kaiA-OX strategy can also be used to enhance the expression ofheterologous genes, resulting in the accumulation of foreign proteins.Bacterial luciferase is an example of a foreign protein that isexpressed well in S. elongatus as a reporter of promoter activity (e.g.,FIG. 6). Moreover, our kaiA-OX strategy up-regulates the accumulation ofLuxAB protein very significantly (nearly 7-fold in the experimentdepicted in FIGS. 10A & 10B). As indicated above, hydrogenase is aprotein of biotechnological interest, but because photosynthesisgenerates oxygen, production-scale generation of H₂ by photosyntheticmicrobes will ultimately require exogenous hydrogenases that are moretolerant of oxygen. While [FeFe] and [Fe]-hydrogenases are rapidlyinactivated by oxygen, [NiFe]-hydrogenases are more active in thepresence of photosynthetically produced oxygen. Fritsch et al., NatureRev. Microbiol. 11, 106-114 (2013). Recently, heterologous expression ofa [NiFe]-hydrogenase from Alteromonas macleodii Deep Ecotype withtolerance to partial oxygen was demonstrated in S. elongatus, generatinga strain called RC41. Weyman et al., PLoS ONE 6, e20126 (2011). RC41features a knockout of the endogenous hoxYH genes encoding thebidirectional [NiFe] hydrogenase (HoxYH), and the trcp-driven expressioncluster encoding the A. macleodii [NiFe] hydrogenase HynSL and other 11surrounding accessory proteins were expressed from the NS I site underthe control of trcp as shown in FigurellA. Generally, two subunits (ca.60 kDa and 30 kDa) are involved in the catalytic core of [NiFe]hydrogenases, and the larger subunit contains the [NiFe] catalytic sitethat requires an extensive set of accessory proteins to assemble anactive catalytic site. Bock et al., Adv. Microb. Physiol. 51, 1-71(2006). While the RC41 strain achieves some hydrogenase activity, lowexpression of the multiple hydrogenase & accessory protein genes wasproblematic.

To test if KaiA can stimulate the expression of the foreign [NiFe]hydrogenase from A. macleodii in S. elongatus, we introduced thetrcp::{ATG}kaiA construct into the NS II site of the RC41 strain andexamined the abundance of the large subunit, HynL, as a marker forexpression of the foreign A. macleodii hydrogenase cassette. We foundthat neither deletion of endogenous hoxYH genes nor overexpression of A.macleodii hydrogenase cluster genes affected the period or phase of theclock in S. elongates (FIG. 11B). When kaiA was additionally expressedin the RC41 strain (+20 μM of IPTG), the abundance of the foreign A.macleodii hydrogenase large subunit, HynL, significantly increasedrelative to a control strain without the trcp::{ATG}kaiA expressioncassette (FIGS. 10C & 10D). Immunoblot assays confirmed that kaiA-OXalso enhanced KaiC protein levels in the hoxYH-null mutant strainco-expressing A. macleodii hydrogenase cluster genes and trcp::{ATG}kaiA(FIG. 10C; FIG. 11C). Compared to the native hydrogenase activity inwild-type S. elongatus, the activity of the foreign A. macleodiihydrogenase in the RC41 strain is lower (FIG. 10E), and thereforemethods to further enhance activity would be necessary before thisstrategy could be useful industrially. We conjecture that part of thedifficulty could be that this hydrogenase operon is so large (about 13kb) that not all of the genes are expressed well. Additionally, theremay be post-transcriptional constraints to overcome so as to achievehigher hydrogenase activity in vivo in S. elongatus. Nevertheless,overexpression of kaiA increased approximately twofold the activity ofH₂ production from the foreign [NiFe] hydrogenase as well as HynLabundance in the RC41 strain (FIG. 10C-10E).

As an another example illustrating how manipulation of kaiA expressioncan enhance production of foreign proteins in cyanobacteria, wegenerated a GST::HPI/KaiA strain, in which a fusion protein between theforeign gene encoding human proinsulin (HPI) and the glutathioneS-transferase (GST) tag was expressed under the control of thenon-cyanobacterial promoter conIIp in NS I, and the expression cassettetrcp::{ATG}kaiA was cloned into NS II (FIG. 11D). Under both light:dark(LD) and LL conditions, kaiA-OX increased production of the foreignGST::HPI fusion protein (FIGS. 10F & 10G; FIGS. 11E and 11F). We noticedthat the accumulation of GST::HPI was particularly high in the darkportion of LD (FIGS. 10F & 10G), so we tested the expression underconstant darkness (DD) and found that kaiA-OX significantly enhanced theaccumulation of GST::HPI in extended darkness (FIGS. 10H & 10I), whichwas unexpected given that S. elongatus is an obligate photoautotroph.

Discussion

The circadian rhythm of KaiC phosphorylation regulates the globalpatterns of gene expression in S. elongatus. The peak and trough levelsof the KaiC phosphorylation rhythm can be mimicked by overexpression ofKaiA or KaiC, respectively (FIG. 12A). Therefore, the opposing actionsof kaiA-OX vs. kaiC-OX form a “Yin-Yang” action, by analogy to theTaoist concept of inverse forces that complementarily interact to form agreater whole (FIGS. 12A & 12B). Increased KaiA levels stimulate KaiCphosphorylation and inhibits KaiC dephosphorylation, thereby promotingKaiC hyperphosphorylation and expression of dusk (Class I) genes (FIG.12B). In the usual post-translational oscillator (PTO) cycle,hyperphosphorylated KaiC interacts with KaiB to form a KaiA/KaiB/KaiCcomplex that allows KaiC to dephosphorylate, and this process can beinduced by kaiC-OX, which disturbs the normal stoichiometry of Kai A:B:Cproteins. The phosphorylation status of the PTO then regulatestranscriptional endpoints by output pathways that include SasA, CikA,LabA, RpaA, and RpaB. Taniguchi et al., Proc. Natl. Acad. Sci. USA 107,3263-3268 (2010). Therefore, kaiA-OX vs. kaiC-OX inversely switch theKaiC phosphorylation status and gene expression patterns between dusk(kaiA-OX) and dawn (kaiC-OX) phases (FIGS. 12A & 12B). In addition,constant induction of KaiA or KaiC both lead to arhythmic expressionpatterns (FIG. 12A).

Our experimental observations led us to re-evaluate the claim that the“negative element” KaiC is a global repressor of gene expression. Infact, microarray analyses of the impact of kaiC-OX on gene expression inS. elongatus in conjunction with our examination of kaiA-OX hereinreveal that BOTH KaiA and KaiC can repress AND enhance transcriptabundances, and that they appear to have opposite effects on theexpression of many genes (FIGS. 2 & 4; FIGS. 3A and 3B). Why then did itappear that KaiC is a global repressor of promoter activities? Nakahiraet al., Proc. Natl. Acad. Sci. USA 101, 881-885 (2004). That conclusionwas based upon the insertion of many different randomly chosen promotersinto neutral site I (NSI). That particular site in the S. elongatusgenome (position 2578661) is downregulated by kaiC-OX and up-regulatedby kaiA-OX (FIG. 3C). We suggest that the neutral site chosen for therandom promoter analysis is topologically regulated by the circadiansystem so that any promoter placed in that site is repressed by KaiC andenhanced by KaiA as a Class I gene independently of how the promoter isregulated in situ.

We exploit these insights into the fundamental regulation of geneexpression in S. elongatus to propose a strategy for maximizing theexpression of genes that encode industrially useful products, wherenon-rhythmically “latching” production at the peak level would beoptimal. In this investigation, we report that overexpression of kaiAup-regulates many endogenous genes in situ as well as foreign genesexpressed from NS I and NS II. Moreover, kaiA-OX attenuates thecircadian rhythm, so that latching of expression at the circadian peaklevel for many genes is achievable. Surprisingly, this reprogramming ofcircadian expression patterns does not appear to have significant impactupon growth rates of S. elongatus in constant light. Therefore, enhancedaccumulation of a useful product would be expected with kaiA-OX (comparethe blue cross-hatched area with the pink area in FIG. 12C).

In addition to the impact of kaiA-OX on expression levels of foreigngenes expressed from NS I or NS II, the suppression of the circadianrhythm by kaiA-OX can also be advantageous if production ofbioindustrial molecules or other gene products is conducted over agrueling 24 h/day, 7 days/week schedule (i.e., “24/7”) under constantillumination. Consistent expression over 24 h with cells maintained inLL opens the possibility of creating bioproduct in both the day phaseand the night phase (S. elongatus cells are normally quiescent in thenight phase), thereby boosting yield (FIG. 12C). The data of FIG.10F-10I also suggest that the expression of some foreign proteins may bestronger in the dark in combination with kaiA-OX. Because thetranscription & translation of most endogenous genes is shut down duringthe dark in S. elongates (Tomita, et al., Science 307, 251-254 (2005)),this may allow the new synthesis that occurs in darkness to bepreferentially weighted to that of foreign genes of industrial interest.We show here the application of stimulating the production of biofuel-and pharmaceutical-related proteins, but this tactic can be potentiallyused to increase expression of any protein or pathway of industrialimportance. Moreover, the overall principle of inactivating thecircadian system so that it latches at the peak expression is notrestricted to cyanobacteria, but may be useful for 24/7 industrialapplications with any organism that has a circadian clock, includingeukaryotic organisms where the circadian system regulates 10-20% of thegenome (e.g., transgenic expression in plants as “bioreactors”).

Example 2: Further Studies of Circadian Regulation Involving a DoubleKaiC Mutation and ΔCikA Knockout

Additional work was carried out to demonstration the effect of mutationof clock genes or clock-related genes on gene expression. FIG. 13 showsthat in addition to overexpression of the positive clock component KaiA,manipulation of mutant versions of the negative component KaiC alsoconstantly enhances gene expression (in this case, the mutant versionsKaiC/A422V/H423N (SEQ ID NO: 12) and KaiC/EE (SEQ ID NO: 13)). Besidesexperimental manipulation of central clock genes such as KaiA and KaiC,FIG. 14 illustrates that manipulation of other clock-related genes canresult in constant high expression of reporter gene even without anyinduction or special treatment. In this particular example, it is thedeletion of an input pathway gene of the circadian system, called cikA(SEQ ID NO: 14), that results in constant high expression of the outputgene.

The complete disclosure of all patents, patent applications, andpublications, and electronically available material cited herein areincorporated by reference. The foregoing detailed description andexamples have been given for clarity of understanding only. Nounnecessary limitations are to be understood therefrom. The invention isnot limited to the exact details shown and described, for variationsobvious to one skilled in the art will be included within the inventiondefined by the claims.

1. A method of increasing gene expression by manipulating the circadianclock, comprising transforming a photosynthetic organism with (a) afirst promoter and a clock gene, wherein the first promoter results inoverexpression of the clock gene to which the first promoter is operablylinked, and (b) a second promoter and a target gene to which the secondpromoter is operably linked, thereby resulting in a change to thecircadian cycle of the cyanobacteria that increases expression of atarget gene, wherein the second promoter is regulated by a clocksignal-transmitting gene, wherein the target gene is not luciferase, andwherein the photosynthetic organism comprises a clocksignal-transmitting gene under the control of an expression controlsequence, wherein the clock-signal transmitting gene exhibits alteredactivity as compared to the natural photosynthetic organism.
 2. Themethod of claim 1, wherein the photosynthetic organism is a plant. 3.The method of claim 1, wherein the photosynthetic organism is aphotoautotrophic or photoheterotrophic bacteria.
 4. The method of claim1, wherein the photosynthetic organism is a cyanobacteria.
 5. The methodof claim 4, wherein the cyanobacteria is Synechococcus elongatus.
 6. Themethod of claim 1, wherein the clock gene is selected from the groupconsisting of KaiA, KaiB, and KaiC.
 7. The method of claim 1, whereinthe clock signal-transmitting gene is SasA, CikA, LabA, RpaA, or RpaB.8. The method of claim 1, wherein modulation of the clocksignal-transmitting gene exhibits altered expression and the expressioncontrol sequence comprises a knockout mutation or a sequence mutationthat alters the activity of clock signal-transmitting gene, wherein theclock gene is selected from KaiA, KaiB, and KaiC (SEQ ID NO: 3, SEQ IDNO: 4, and SEQ ID NO: 5) and the clock signal-transmitting gene isselected from SasA, CikA, LabA, RpaA and RpaB.
 9. The method of claim 1,wherein the clock signal-transmitting gene comprises a deletionmutation.
 10. The method of claim 9, wherein deletion mutation is aknock out.
 11. The method of claim 1, wherein modulating expression of aclock gene suppresses the circadian rhythm of the photosyntheticorganism.
 12. The method of claim 1, wherein the target gene is abiofuel product or biofuel precursor expressing gene.
 13. The method ofclaim 1, wherein the photosynthetic organism is a transgenicphotosynthetic organism, and the target gene is a heterologous gene. 14.The method of claim 13, wherein the heterologous gene is a hydrogenaseexpressing gene.
 15. The method of claim 13, wherein the heterologousgene is a pro-insulin expressing gene.
 16. A photosynthetic organismhaving a modified circadian cycle, comprising a photosynthetic organismthat has been transformed to with (a) a first promoter and a clock gene,wherein the first promoter results in overexpression of the clock geneto which the first promoter is operably linked, and (b) a secondpromoter and a target gene to which the second promoter is operablylinked, thereby resulting in a change to the circadian cycle of thecyanobacteria that increases expression of a target gene, wherein thesecond promoter is regulated by a clock signal-transmitting gene,wherein the target gene is not luciferase, and wherein thephotosynthetic organism underexpresses a clock signal-transmitting geneas compared to the natural photosynthetic organism.
 17. Thephotosynthetic organism of claim 16, wherein the photosynthetic organismis a plant.
 18. The photosynthetic organism of claim 16, wherein thephotosynthetic organism is a photoautotrophic or photoheterotrophicbacteria.
 19. The photosynthetic organism of claim 18, wherein the clockgene is selected from the group consisting of KaiA, KaiB, and KaiC. 20.The photosynthetic organism of claim 16, wherein modulating expressionof a clock gene suppresses the circadian rhythm of the photosyntheticorganism.
 21. The photosynthetic organism of claim 16, wherein thetarget gene is a gene influencing the expression of a biofuel product orbiofuel precursor.
 22. The photosynthetic organism of claim 16, whereinthe photosynthetic organism is a transgenic photosynthetic organism, andthe target gene is a heterologous gene.
 23. The method of claim 16,wherein the clock signal-transmitting gene is SasA, CikA, LabA, RpaA, orRpaB.